Yes I have had this happen multiple times in the past. I think there is something that triggers it. It seems like selecting the faction you intend to trade the region to and (accidentally) opening the regular diplomacy page, closing the regular diplomacy, then opening the trade regions window resets the faction you are negotiating with. I am playing as the Abbasids right now so the Almohads were the faction it is resetting to for me. So, yes, I think it is resetting to the top of the list. I quick save immediately before giving away regions now.